User: F. Golestan
F. Golestan • 20
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Posts by F. Golestan
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... Dear Leite,
Thank you so much for your great help and support. That was perfect. Your help and patience is highly appreciated. Best regards. ...
written 1 day ago by
F. Golestan • 20
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... Hello,
May I kindly ask you to let me know how can I also add to the above bar chart a vertical red line which shows a threshold (such as for example 0.05 p-value as a threshold of significance). I need to create a bar chart like the attached figure.
I assume that the red line, in the attached im ...
written 3 days ago by
F. Golestan • 20
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... Dear Leite,
Thank you so much for your great help and guide. Your guides helped me a lot.
As you suggested, I used STRING db with my parameters (only experiment, and confidence score of 0.4). I then exported
TSV: tab separated values and imported into cytoscape (File -> Import -> Network fro ...
written 4 days ago by
F. Golestan • 20
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... Hello,
I found this paper "https://www.nature.com/articles/s41556-018-0220-2" very useful for my research. I read their paper and supplementary materials. However, in their protein-protein interaction network of Figure 5 ![p-p network][1], I could not understand how they inferred that a protein in ...
written 4 days ago by
F. Golestan • 20
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... Dear Leite,
Many thanks for your guide. Actually, before, I was using StringApp for pulling ppi networks. But, firstly, by using StingApp, I can not choose to retrieve only experimentally validated interactions (as it is possible in original String database). Secondly, I do not know how to detect "d ...
written 4 days ago by
F. Golestan • 20
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... Hello,
I found a paper (https://www.nature.com/articles/s41556-018-0220-2#Fig5) that they created STRING protein-protein network and also gene ontology bar charts as in their Figure 5.
![Fig. 5: Mass spectrometry reveals the distinct reticular adhesome.][1]
May I kindly ask you to let me have yo ...
written 5 days ago by
F. Golestan • 20
• updated
3 days ago by
Leite • 850
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... Many thanks for your helpful explanations. I got the points. Thanks a lot. ...
written 6 days ago by
F. Golestan • 20
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... Hello,
I am using Seurat package for the analysis of my single-cell RNA-seq. I read their basic PBMCs tutorial https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html. However, I get confused about some steps. I would highly appreciate having your answers on my following questions:
1) Is FindVari ...
written 7 days ago by
F. Golestan • 20
• updated
7 days ago by
jared.andrews07 • 3.7k
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... Thank you very much for your help.
I also found another way of doing kallisto bus for many fastq files at once as below:
cd /scratch/fsgh1d18/kallisto_bustools_multiple_lanes/fastqs/
kallisto bus -i /scratch/fsgh1d18/kallisto_bustools_multiple_lanes/Mus_musculus.GRCm38.cdna.all.idx -o ...
written 25 days ago by
F. Golestan • 20
0
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... Thanks. The result of running the code with "*_001.fastq.gz" (instead of "*_[R1R2]_001.fastq.gz") is as below:
FILEBASE
kallisto bus -i /scratch/fsgh1d18/kallisto_bustools_multiple_lanes/Mus_musculus.GRCm38.cdna.all.idx -x 10xv2 -o . -t 16 /scratch/fsgh1d18/kallisto_bustools_multiple_lanes ...
written 27 days ago by
F. Golestan • 20
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5.9 years ago,
created a question with more than 1,000 views.
For Need Help In Rcircos Package In R Software.
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